Three-Dimensional Structure of Fab Fragment of Monoclonal Antibody LNKB-2 Complexed with Antigenic Nonaptide from Human Interleukin-2

E. A. Goryacheva; Горячева Е. А.; I. V. Artemyev; Артемьев И. В.; N. V. Pletnevа; Плетнева Н. В.; V. Z. Pletnev; Плетнев В. З.

doi:10.31857/S0132342323010098

Three-Dimensional Structure of Fab Fragment of Monoclonal Antibody LNKB-2 Complexed with Antigenic Nonaptide from Human Interleukin-2

Authors: Goryacheva E.A.¹, Artemyev I.V.¹, Pletnevа N.V.¹, Pletnev V.Z.¹
Affiliations:
1. Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences
Issue: Vol 49, No 3 (2023)
Pages: 285-290
Section: Articles
URL: https://rjmseer.com/0132-3423/article/view/670613
DOI: https://doi.org/10.31857/S0132342323010098
EDN: https://elibrary.ru/GFDHZS
ID: 670613

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Abstract
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Abstract

The three-dimensional structure of the antigen-binding fragment (Fab) of the monoclonal antibody LNKB-2 in complex with the synthetic antigenic nonapeptide of human interleukin-2 (IL-2; Lys-Pro-Leu-Glu-Glu-Val-Leu-Asn-Leu-O) was determined by X-ray method at a resolution of 2.6 Å in crystal space group P2₁2₁2₁. The peptide adopts a somewhat distorted α-helical conformation, close to that of fragment 64–72 of the IL-2 antigen. Four out of the six hypervariable loops in the antigen-binding site of the Fab fragment are involved in nonapeptide association through hydrogen bonding, salt bridge formation, and hydrophobic interactions. Moreover, Tyr residues of an antibody play an important role in antigen-antibody recognition.

Keywords

monoclonal antibody, Fab fragment, interleukin-2 antigen, three-dimensional structure, X-ray study

References

Sela-Culang I., Kunik V., Ofran Y. // Front. Immunol. 2013. V. 4. P. 302. https://doi.org/10.3389/fimmu.2013.00302
Burkovitz A., Leiderman O., Sela-Culang I., Byk G., Ofran Y. // J. Immunol. 2013. V. 190. P. 2327–2334. https://doi.org/10.4049/jimmunol.1200757
Kapingidza A.B., Kowal K., Chruszcz M. // Subcell. Biochem. 2020. V. 94. P. 465–497. https://doi.org/10.1007/978-3-030-41769-7_19
King M.T., Brooks C.L. // Methods Mol. Biol. 2018. V. 1785. P. 13–27. https://doi.org/10.1007/978-1-4939-7841-0_2
Smith K.A. // Science. 1988. V. 240. P. 1169–1176. https://doi.org/10.1126/science.3131876
Smith K.A. // Curr. Opin. Immunol. 1992. V. 4. P. 271–276. https://doi.org/10.1016/0952-7915(92)90076-q
Lunev V.E., Lukin Yu.V., Kazannykh N.V., Belyaev S.V., Zubov V.P., Nesmeyanov V.A. // Biomed. Sci. 1990. V. 1. P. 68–72.
Фокин A.В., Афонин П.В., Михайлова И.Ю., Цыганник И.Н., Мареева Т.Ю., Несмеянов B.А., Пэнгборн В., Ли Н., Дюэкс В., Сижак Е., Плетнев В.З. // Биоорг. химия. 2000. Т. 26. С. 571–578. [Fokin A.V., Afonin P.V., Mikhailova I.Yu., Tsygannik I.N., Mareeva T.Yu., Nesmeyanov V.A., Pangborn W., Lee N., Duax W., Ciszak E., Pletnev V.Z. // Russ. J. Bioorg. Chem. 2000. V. 39. P. 512–519.] https://doi.org/10.1007/BF02758622
Плетнев В.З., Горячева Е.А., Цыганник И.Н., Несмеянов В.А., Плетнев С.В., Пэнгборн В., Дюэкс В. // Биоорг. химия. 2004. Т. 30. С. 466–469. [Pletnev V.Z., Goryacheva E.A., Tsygannik I.N., Nesmeyanov V.A., Pletnev S.V., Pangborn W., Daux W. // Russ. J. Bioorg. Chem. 2004. V. 30. P. 417–420.] https://doi.org/10.1023/b:rubi.0000043783.73562.ef
Afonin P.V., Fokin A.V., Tsygannik I.N., Mikhailova I.Yu., Onoprienko L.V., Mikhaleva I.I., Ivanov V.T., Mareeva T.Yu., Nesmeyanov V.A., Li N., Pangborn W.A., Duax W.L., Pletnev V.Z. // Protein Sci. 2001. V. 10. P. 1514–1521. https://doi.org/10.1110/ps.3101
Kabat E.A., Wu T.T., Perry H.M., Gottesman K.S., Foeller C. // Sequences of Proteins of Immunological Interest, 5th ed. U.S. Department of Health and Human Services, Public Health Service, National Institutes of Health, Bethesda, 1991.
Оноприенко Л.В., Михалева И.И., Иванов В.Т., Войтенков Б.О., Окулов В.Б. // Биоорг. химия. 1996. Т. 22. С. 180–190. [Onoprienko L.V., Mikhaleva I.I., Ivanov V.T., Voitenkov B.O., Okulov V.B. // Russ. J. Bioorg. Chem. 1996. V. 22. P. 156–165.]
Vagin A., Teplyakov A. // Acta Crystallogr. D Biol. Crystallogr. 2010. V. 66. P. 22–25. https://doi.org/10.1107/S0907444909042589
Murshudov G.N., Skubák P., Lebedev A.A., Pannu N.S., Steiner R.A., Nicholls R.A., Winn M.D., Long F., Vagin A.A. // Acta Crystallogr. D Biol. Crystallogr. 2011. V. 67. P. 355–367. https://doi.org/10.1107/S0907444911001314
Emsley P., Lohkamp B., Scott W.G., Cowtan K. // Acta Crystallogr. D Biol. Crystallogr. 2010. V. 66. P. 486–501. https://doi.org/10.1107/S0907444910007493